Small scale manufacturing is an important aspect of the modern economy. For example, tip based fabrication can be used to make micro-, nano-, and atomic scale structures. Examples of interest include dots and lines in various shapes and patterns, multi-layer structures, quantum dots, nanoparticles, nanowires, nanotubes, and carbon nanotubes. Direct write methods are useful wherein a pattern can be directly drawn or embedded into a substrate surface. In one embodiment, material is transferred from a tip to a substrate using, for example, one or more nanoscopic, scanning probe, or atomic force microscope tips. Fabrication can be carried out to make a variety of structures including soft and hard structures, organic and inorganic structures, and biological structures. Imaging of structures on the small scale is also important. Instruments and devices can be fabricated which allow for both imaging and fabrication. See, for example, U.S. Pat. No. 7,253,408. Despite important advances, a need exists—particularly for commercial applications—to provide better devices and instruments which enable a broader array of fabrication methods, e.g., use of high temperatures or use of corrosive gases.